USA flag logo/image

An Official Website of the United States Government

Incorporating microRNA data and analyses into the leading cancer genomics portal

Award Information

Agency:
Department of Health and Human Services
Branch:
N/A
Award ID:
95947
Program Year/Program:
2010 / SBIR
Agency Tracking Number:
CA153974
Solicitation Year:
N/A
Solicitation Topic Code:
NCI
Solicitation Number:
N/A
Small Business Information
COMPENDIA BIOSCIENCE, INC.
110 MILLER AVE, 2ND FL ANN ARBOR, MI 48104-
View profile »
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
 
Phase 1
Fiscal Year: 2010
Title: Incorporating microRNA data and analyses into the leading cancer genomics portal
Agency: HHS
Contract: 1R44CA153974-01
Award Amount: $1,325,222.00
 

Abstract:

DESCRIPTION (provided by applicant): Micro-RNAs (miRNAs) are small non-coding RNAs that control gene expression by regulating messenger (mRNA) translation. miRNAs can act as oncogenes or tumor suppressors, and the differential expression of miRNAs has been correlated with cancer diagnosis, staging, and prognosis, and has been used to nominate therapeutic targets. Much of what is known about miRNAs in cancer comes from genome-scale miRNA expression profiling. Unfortunately, despite hundreds of published stud ies using miRNA profiling data, at present a basic cancer biologist lacks tools to survey the differential expression of one or more miRNAs in a specific cancer type or across the global collection of miRNA expression profiling studies. Barriers include id entifying available data, platform heterogeneity, analysis methods and meaningful presentation of results. Thus, a useful solution must address a number of challenges, including the growing number of miRNAs, multiple technologies and reporters used to meas ure miRNA expression, disparate clinical and experimental facts, and producing biologically meaningful analyses. Here we propose to develop a solution for a biologist seeking to explore a single miRNA or a miRNA signature across the global collection of ca ncer miRNA data sets. To accomplish this, our overall goal is to collect all publicly available cancer-related high throughput miRNA data, to standardize the disparate data at three levels - sample data, expression data, and statistical analyses - and to p resent the data in a consistent, comparable format that is also fully integrated with existing, mRNA and DNA copy data in Oncomine. In Phase I we will 1) Establish and implement sample metadata curation strategy for 3 micro-RNA profiling datasets to demons trate feasibility of applying a controlled vocabulary and ontology to miRNA sample metadata; 2) Establish and implement platform mapping strategy for 3 micro-RNA profiling datasets to demonstrate feasibility of standardizing disparate miRNA platforms into a single, unified format; 3) Perform differential expression analysis on 3 micro-RNA profiling datasets to demonstrate feasibility of creating automatically standardized analyses following the curation and mapping steps conducted in Aims 1 and 2. Upon succ essful completion of Phase I, we propose the following Phase II aims: 1) Development and Implementation of a scalable process for capturing and curating micro-RNA genomics data and integration into Oncomine by developing software to support the scalable ca talog and capture of miRNA sample data; 2) Development of a scalable micro-RNA genomics platform mapping and data warehouse strategy and integration into Oncomine, by developing tools to accommodate dynamic naming conventions for micro-RNAS and mapping to common identifiers, and 3) Development of automated analysis methods for analyzing micro-RNA profiling datasets and integration into Oncomine by developing automated differential expression, co-expression, outlier, and meta- analysis capability across the miRNA database, and integration within the established Oncomine database. PUBLIC HEALTH RELEVANCE: Despite the substantial efforts of scientist to understand the molecular basis of cancer, these research gains have been difficult to translate into c linical practice, and cancer remains a leading cause of mortality in the United States. This proposal seeks to make micro-RNA data - which is clearly correlated with cancer diagnosis, staging, and prognosis - easily accessible to cancer researchers via the cancer genomic portal Oncomine. If successful, this effort will improve public health by providing researchers with additional data and tools to understand and treat this biologically complex disease.

Principal Investigator:

Daniel R. Rhodes
7349040365
DRHODES@COMPENDIABIO.COM

Business Contact:

Colleen B. Kincaid
ckincaidbeal@compendiabio.com
Small Business Information at Submission:

COMPENDIA BIOSCIENCE, INC.
COMPENDIA BIOSCIENCE, INC. 110 MILLER AVE, 2ND FL ANN ARBOR, MI 48104

EIN/Tax ID: 120415482
DUNS: N/A
Number of Employees: N/A
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No